2013 - 2015 News

This newsletter is published in partnership between The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca) and the international Metabolomics Society (http://www.metabolomicssociety.org), and is intended to keep metabolomics researchers and other professionals informed about new technologies, software, databases, events, job postings, conferences, training opportunities, interviews, publications, awards, and other newsworthy items concerning metabolomics.

We now have a dedicated section in MetaboNews for monthly updates on Status of Data Standards:This new section within the Metabolomics Society News will be contributed regularly by Christoph Steinbeck (Chair of the Society’s Data Standards Task Group) and Reza Salek from the EMBL-EBI, Cambridge UK.

MetaboNewsDecember issue: Status of Data Standards: The COordination of Standards in MetabOlomicS (COSMOS) consortium (http://www.cosmos-fp7.eu) together with Proteomics Standards Initiative (PSI) is working towards completing the existing mzTab format (http://www.psidev.info/) to better capture small molecules data and meta-data. mzTab can be used for reporting both metabolite identification and metabolomics quantification. After extensive research and discussions within the consortium and members of the MSI and PSI community, we concluded that mzTab is the medium of choice for capturing and reporting such metabolomics results. To test and evaluate the standard, the mzTab development is accompanied by early implementations, e.g., in development versions of the OpenMS (http://open-ms.sourceforge.net/), or separate export functions for XCMS and CAMERA (http://www.bioconductor.org/) software tools. In addition, the MetaboLights metabolomics database (http://www.ebi.ac.uk/metabolights) accepts the quantification and identification of metabolites in a subset of mzTab, soon to be updated to the full compatible version, once the final discussions on the mzTab format for small molecules are completed. We are planning to have an “mzTab for metabolomics” workshop in Tübingen (in March 2014) for discussion and work on metabolomics extensions for mzTab. We hope to adopt and finalize the format and eventually submit it to the community for review. The workshop is organised jointly by Steffen Neumann (Leibniz Institute of Plant Biochemistry, IPB Halle) and Oliver Kohlbacher (Tübingen University), one of the leading members in the mzTab development in the PSI. For details, please visit http://cosmos-fp7.eu/mzTab.

MetaboNews January issue: Status of Data Standards: One of the aims of the COordination of Standards in MetabOlomicS (COSMOS) consortium (http://www.cosmos-fp7.eu) is to gather metabolomics requirements for other major e-infrastructures such as BioMedBridges (http://www.biomedbridges.eu/), BBMRI (http://bbmri.eu/), ELIXIR (http://www.elixir-europe.org/) and EU-OPENSCREEN (http://www.eu-openscreen.de/). The University of Florence as a third party of CIRMMP (http://www.cerm.unifi.it/about-cerm/cirmmp) coordinates the gathering and requirements of metabolomics data with the above-mentioned e-infrastructures. Coordination with BioMedBridges and biomedical ESFRI infrastructures (the European Strategy Forum on Research Infrastructures), aims to foster their co-operation and interaction with COSMOS. The interaction with BioMedBridges occurred through the participation of COSMOS delegates at meetings and workshops organized by the BioMedBridges. Strong interactions between COSMOS and BBMRI have been established to coordinate efforts. For this reason, Kurt Zatloukal, coordinator of BBMRI has been nominated among the Advisory Board of COSMOS. The ELIXIR Hub will be connected to ELIXIR Nodes to provide infrastructure for data, computing tools and standards as well as training and support for the ESFRI biological and medical science infrastructures. The link from COSMOS to ELIXIR is via MetaboLights (http://www.ebi.ac.uk/metabolights/); an open access repository housing metabolomics-based experiments. The coordination outcome will be published on the COSMOS (http://www.cosmos-fp7.eu) website.

MetaboNews February and March issue: Status of Data Standards: Development of nmrML format: Currently, the most widely used data exchange format for NMR data is JCAMP-DX version 6.0 by the Joint Committee on Atomic and Molecular Physical Data (Davies and Lampen, 1993), but the specification is not very rigorous and many different flavors exist in the wild, which can lead to incompatibilities between different software packages. It is also not easily extendable to capture supplementary information. The MSI workgroups have provided detailed suggestions about the minimum information metadata to be captured for a NMR experiment. In particular, the MSI, had put forth recommendations to report instrument descriptions and configurations, instrument-specific sample preparation and data acquisition parameters (Rubtsov, Jenkins et al., 2007), which resulted in a first round of NMR XML data standard development, focusing on raw and processed one- and two-dimensional NMR experiments and associated metadata (Ludwig, Easton et al., 2012). Inspired by the huge success of mzML in mass spectrometry, the COSMOS COordination Of Standards In MetabOlomicS (http://cosmos-fp7.eu) consortium has joined forces with other groups and has now merged and adopted existing schemata into a new nmrML format (http://nmrml.org). The format consists of the XML schema that defines the structure of an nmrML file. This structure is deliberately kept simple to ease the task of implementation, and avoid the need for frequent changes when the terminology needs to accommodate upcoming new technologies and parameters. Instead, these will be annotated in the nmrML file using the second component of nmrML, the controlled vocabulary terms from the nmrCV ontology. The nmrCV is based on earlier work at the EMBL-EBI (Sansone, Schober et al., 2007) and efforts at The Metabolomics Innovation Centre (David Wishart Group). The nmrCV contains nearly 600 terms and partly relies on external sources like ChEBI for chemical information, thus making it an integrative resource. Term request can be channeled through the issue tracker/mailing list. We also provide early prototypes for file converters from vendor formats to nmrML, as well as parser libraries for Java, R and python, which can be used by open NMR processing and analysis software. The development of nmrML is taking place on Github (https://github.com/nmrML/nmrml), where the specification documents, more detailed descriptions of our use cases, examples files and the parser libraries can be found. We are now providing a first nmrML release candidate at http://nmrml.org for public consultation and feedback.

MetaboNews April issue: Status of Data Standards: Joint COSMOS and HUPO PSI Meeting: In April 13-16 the COSMOS (COordination Of Standards In MetabOlomicS) is planning to participate and to have a joint meeting with the proteomics HUPO Proteomics Standards Initiative community. This meeting will take place in Schloss Reinhartshausen Kempinski, Nr Frankfurt, Germany. HUPO-PSI has defined community standards for data representation in proteomics and has facilitated data comparison, exchange and verification within the proteomics community. Many open source MS formats including: mzML, mzTab, mzIdentML and mzQuantML as well as guidelines for minimum information reporting for proteomic and peptide identification have been developed within this initiative. Working closely with the HUPO-PSI community should benefit the metabolomics community, particularly the COSMOS effort in development of open MS exchange formats for metabolomics. We also hope to contribute to the development of the MS-based controlled vocabulary by PSI-MS by adding the metabolomics community ontology requirement and terminology artifacts. More details can be found at: http://cosmos-fp7.eu/PSI and http://www.psidev.info/psi2014

ABSTRACT MetaboLights - The new EBI Metabolomics database. Over the past ten years a significant number of databases for Metabolomics have been created, differing in the types of data, species and applications they cover. Recently, efforts are underway to establish large-scale repositories for metabolomics data as they exist for the other omics areas, both in Europe as well as in the United States.

MetaboNews: September 2013: Metabointerview with Dr Tim Ebbels, highlights work of COSMOS.

MetaboNews July 2014: Metabolomics Data Interoperability Interest Group (https://www.rd-alliance.org/group/metabolomics.html) has been formed as part of the Research Data Alliance (RDA, https://www.rd-alliance.org/). The RDA is dedicated to enabling open data sharing in science and is supported by, for example, the National Science Foundation (NSF) in the USA and the European Commission.The Metabolomics Data Interoperability Interest Group (IG) in the RDA aims to provide a forum to discuss all aspects of metabolomics data management and harmonisation. The initial membership of the Metabolomics Data Interoperability IG is drawn from the leaders of several internationally recognised research programmes that are developing metabolomics databases and from the international Metabolomics Society’s Board of Directors. It encourages a broad group of researchers, technologists, and curators to join as members to address issues of data interoperability and sharing in metabolomics. Currently, the interest group is chaired by Christoph Steinbeck, whose team develops the MetaboLights database at EMBL-EBI in Hinxton, as well as Shankar Subramaniam, leader of the Metabolomics workbench project in the US.In particular, this IG will address interoperability of databases and the coordination of standards. In addition, there are obvious synergies with other existing technical and domain specific Interest Groups and Working Groups in the Research Data Alliance, including (but not limited to) the Big Data Analytics IG, Data Foundation and Terminology Working Group, or the Toxicogenomics IG.

MetaboNews August 2014: A workshop was organized by COSMOS and the Data Standards Task Group of the Metabolomics Society during the annual Metabolomics Society conference in June held at Tsuruoka, Japan. Reza Salek (EMBL-EBI, UK) presented the current status and on-going developments worldwide on data standards, particularly the role of COSMOS (http://www.cosmos-fp7.eu). Steffen Neumann (Leibniz IPB, Halle Germany) gave an overview of data exchange formats in MS and how to get the users and instrument vendors involved. Philippe Rocca-Serra (Oxford e-Research Centre, UK) presented ISA-Tools for capturing metabolomics metadata, semantics and usage of RDF in metabolomics. In the second session, Scott Edmunds and Rob Davidson (GigaScience, Hong Kong) presented the Gigajournal point of view on publishing metabolomics data and workflows with the GigaScience, GigaDB and GigaGalaxy platforms. Susanna-Assunta Sansone (Nature Scientific Data) introduced NScD’s role in placing importance on data and the role that the NScD is playing on putting value in your datasets. The last two presentations were by Reza Salek and Padma Maruvada (NIH/NIDDK, USA) giving an overview of metabolomics repositories, MetaboLights and NIH Metabolomics WorkBench. We had plenty of interested discussion points on usage and promotion of standard, metabolomics data deposition and dissemination.

In June 2014, also supported by a BBSRC UK-China partnering award (BB/J020265/1), the Biomed Central Gigascience Team at BGI Hong Kong, and the ISA Team at the University of Oxford e-Research Centre organized a hackathon in Hong Kong, with participation of young scientists and ‘-omics’ data producers from local university and the UK metabolomics standards community (EMBL-EBI, COSMOS and Birmingham Metabolomics Centre). The goal was to establish common standards and curation practices for omics data as well implement new ISA software (http://isatab.sourceforge.net) functionalities to facilitate deposition to MetaboLights repository (http://www.ebi.ac.uk/metabolights/) and support feature requests from journal using ISA formats, such as GigaScience (http://www.gigasciencejournal.com) and Scientific Data (http://www.nature.com/sdata/). The fruitful interaction between the participants over the duration of the meeting resulted in the delivery of an ISA-Tab viewing component for web browsers (http://dx.doi.org/10.5281/zenodo.11084 for the code and http://isatab.sourceforge.net/examples.html), and the conversion of MetaboLights ISA-Tab content to RDF. Finally, efforts to deliver an API supporting the programmatic creation of an ISA-Tab document are well under way. Owing to the success on this first ISA-thon event, the same teams will be organizing a follow-up meeting.

MetaboNew December 2014: Spotlight article: nmrML: A vendor-neutral open exchange format for NMR-based metabolomicshttp://www.metabonews.ca/Dec2014/MetaboNews_Dec2014.htm#spotlight
Feature article contributed by Daniel Schober, Michael Wilson, Daniel Jacob, Annick Moing, Catherine Deborde, Kenneth Haug, Philippe Rocca-Serra, John Easton, Tim Ebbels, Jie Hao, Christian Ludwig, Antonio Rosato, David Wishart, Christoph Steinbeck, Reza Salek, Steffen Neumann, and the COSMOS standards developers. Metabolomics is a growing field and the number of organisms being studied is constantly increasing as is the number of metabolites being discovered. With this growth comes a steady increase in the amount of metabolomics data and the need to ensure that we capture this information in persistent open formats and databases. The COSMOS project (COordination Of Standards In MetabOlomicS, http://www.cosmos-fp7.eu/) has been created to improve the adoption of open standards for metabolomics data, annotation with agreed metadata, and support by open source data management and capturing tools. COSMOS delivers an ecosystem of formats, tools, and resources such as MetaboLights (http://www.ebi.ac.uk/metabolights/), a database for capturing information obtained in metabolomics experiments. Here we introduce recent developments in nmrML (www.nmrml.org), a vendor-neutral open exchange and storage format to describe NMR-based metabolomics data

MetaboNew May 2015:Computational MS Task Grouphttp://www.metabonews.ca/May2015/MetaboNews_May2015.htm
The task group “Computational Mass Spectrometry” [1] represents the CompMS [2] initiative in the Metabolomics society. The CompMS initiative promotes the efficient, high quality analysis of mass spectrometry data with state-of-the art computational tools and algorithms through dissemination and training in existing, and coordination of new, innovative approaches. The CompMS initiative aims to exploit synergies between different application domains, in particular proteomics and metabolomics. The scientific remit of the group will include all aspects of computational method development from signal processing, feature alignment and grouping, to development of metabolite identification algorithms and metabolic network reconstruction

The mission is to 1) build a community of scientists working in computational mass spectrometry, 2) integrate experimental and theoretical research, and 3) educate a new generation of computational scientists via training and dissemination of results. The CompMS is a joint initiative between the International Society for Computational Biology (ISCB CoSI CompMS), the Human Proteome Organization and its Computational Mass Spectrometry Initiative (HUPO CompMS), and the Metabolomics Society.